The International Atomic Energy Agency (IAEA) has been founded as a global organization dedicating to monitor international nuclear activities, prevent nuclear proliferation and safeguard the nuclear peaceful use. Since the time of its coming into being, the Nuclear Safeguards System (NSS), which based on nuclear safeguards provisions of the IAEA and underpinned by nuclear Safeguards Model Agreements & Additional Protocol, has gone through an ever-changing and improving process. At the condition of fully admitting the huge and irreplaceable role of the IAEA in preventing nuclear proliferation, promoting peaceful using nuclear energy as widely well known, this paper just tries to focus some limitations of the IAEA which might exist when it implies its nonproliferation function. Some of these limitations are due to the nature of international organization, but some of them may caused by other subjective reasons. The Iran nuclear issue has taken a center of international non-proliferation theatre since 2003. Taking Iran nuclear issue as an example to analysis the limitations of the IAEA, should contribute to strength the role and status of the IAEA in non-proliferation area. There are at least four points need to discuss. How to balance the two wheels of non-proliferation and peaceful use? How to avoid the double-standard phenomenon as far as possible and promote the universality and authority of the IAEA? How to deal with the relationship of relative independence of the IAEA and the last result of UN Security Council (UNSC)? How to look at the relationship of the IAEA and the big powers, i.e. US?
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